scholarly journals redkmer: an assembly-free pipeline for the identification of abundant and specific X-chromosome target sequences for X-shredding by CRISPR endonucleases

2017 ◽  
Author(s):  
Philippos Aris Papathanos ◽  
Nikolai Windbichler
Keyword(s):  
Sex Ratio ◽  
X Chromosome ◽  
Single Molecule ◽  
Sex Chromosome ◽  
Insect Pest ◽  
Gene Array ◽  
Ribosomal Gene ◽  
Long Reads ◽  
Target Sequences ◽  
Harmful Insect

AbstractCRISPR-based synthetic sex ratio distorters, that operate by shredding the X-chromosome during male meiosis, are promising tools for the area-wide control of harmful insect pest or disease vector species. However, the selection of gRNA targets, in the form of high-copy sequence repeats on the X chromosome of a given species, is difficult since such repeats are not accurately resolved in genome assemblies and can’t be assigned to chromosomes with confidence. We have therefore developed the redkmer computational pipeline, designed to identify short and highly-abundant sequence elements occurring uniquely on the X-chromosome. Redkmer was designed to use as input exclusively raw WGS data from males and females. We tested redkmer with suitable short and long read WGS data ofAn. gambiae, the major vector of human malaria, in which the X-shredding paradigm was originally developed. Redkmer establishes long reads as chromosomal proxies with excellent correlation to the genome assembly and uses them to rank X-candidate kmers for their level of X-specificity and abundance. Redkmer identified a high-confidence set of 25-mers, many of which belong to previously known X-chromosome specific repeats ofAn. gambiae, including the ribosomal gene array and the selfish genetics elements harbored within it. WGS data from a control strain in which these repeats are also present on the Y chromosome confirmed the elimination of these kmers in the filtering steps. Finally, we show that redkmer output can be linked directly to gRNA selection and can also inform gRNA off-target prediction. The redkmer pipeline is designed to enable the generation of synthetic sex ratio distorters for the control of harmful insect species of medical or agricultural importance. It proceeds from WGS input data to deliver candidate X-specific CRISPR gRNA candidate target sequences. In addition the output of redkmer, including the prediction of chromosomal origin of single-molecule long reads and chromosome specific kmers, could also be used for the characterization of other biologically relevant sex chromosome sequences, a task that is frequently hampered by the repetitiveness of sex chromosome sequence content.

Sperm Competition and the Dynamics of X Chromosome Drive: Stability and Extinction

Genetics ◽  
2002 ◽  
Vol 160 (4) ◽  
pp. 1721-1731 ◽  
Author(s):  
Jesse E Taylor ◽  
John Jaenike
Keyword(s):  
Sex Ratio ◽  
Sperm Competition ◽  
X Chromosome ◽  
Sex Chromosome ◽  
Basin Of Attraction ◽  
Male Mating ◽  
Male And Female ◽  
Mating Rate ◽  
Female Mating ◽  
Balanced Polymorphism

AbstractSeveral empirical studies of sperm competition in populations polymorphic for a driving X chromosome have revealed that Sex-ratio males (those carrying a driving X) are at a disadvantage relative to Standard males. Because the frequency of the driving X chromosome determines the population-level sex ratio and thus alters male and female mating rates, the evolutionary consequences of sperm competition for sex chromosome meiotic drive are subtle. As the SR allele increases in frequency, the ratio of females to males also increases, causing an increase in the male mating rate and a decrease in the female mating rate. While the former change may exacerbate the disadvantage of Sex-ratio males during sperm competition, the latter change decreases the incidence of sperm competition within the population. We analyze a model of the effects of sperm competition on a driving X chromosome and show that these opposing trends in male and female mating rates can result in two coexisting locally stable equilibria, one corresponding to a balanced polymorphism of the SR and ST alleles and the second to fixation of the ST allele. Stochastic fluctuations of either the population sex ratio or the SR frequency can then drive the population away from the balanced polymorphism and into the basin of attraction for the second equilibrium, resulting in fixation of the SR allele and extinction of the population.

scholarly journals A compendium of novel genomics technologies provides a chromosome-scale assembly and insights into the sex determining system of the Greenland Halibut

2021 ◽  
Author(s):  
Anne-Laure Ferchaud ◽  
Claire Merot ◽  
Eric Normandeau ◽  
Ioannis Ragoussis ◽  
Charles Babin ◽  
...  
Keyword(s):  
Sex Determination ◽  
Single Molecule ◽  
Sex Chromosome ◽  
Major Effect ◽  
Whole Genome Sequence ◽  
Greenland Halibut ◽  
Long Reads ◽  
Full Picture ◽  
High Conservation ◽  
High Level

Despite the commercial importance of Greenland Halibut (Reinhardtius hippoglossoides), important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. In this study, we combined single molecule sequencing of long reads (Pacific Sciences) with Chromatin Conformation Capture sequencing (Hi-C) data to provide the first chromosome-level genome reference for this species. The high-quality assembly encompassed more than 598 Megabases (Mb) assigned to 1 594 scaffolds (scaffold N50 = 25 Mb) with 96 % of its total length distributed among 24 chromosomes. The investigation of its syntenic relationships with other economically important flatfish species revealed a high conservation of synteny blocks among members of this phylogenetic clade. Sex determination analysis revealed that flatfishes do not escape the rule applied to other teleost fish and exhibit a high level of plasticity and turnover in sex-determination mechanisms. A whole-genome sequence analysis of 198 individuals allowed us to draw a full picture of the molecular sex determination (SD) system for Greenland Halibut, revealing that this species possesses a very nascent male heterogametic XY system, with a putative major effect of the sox2 gene, also described as the main SD driver in two other flatfishes. Interestingly, our study also suggested for the first time in flatfishes that a putative Y-autosomal fusion could be associated with a reduction of recombination typical of early steps of sex chromosome evolution.

scholarly journals The potential for a released autosomal X-shredder becoming a driving-Y chromosome and invasively suppressing wild populations of malaria mosquitoes

2019 ◽  
Author(s):  
Yehonatan Alcalay ◽  
Silke Fuchs ◽  
Roberto Galizi ◽  
Federica Bernardini ◽  
Roya Elaine Haghighat-Khah ◽  
...  
Keyword(s):  
Sex Ratio ◽  
Y Chromosome ◽  
X Chromosome ◽  
Sex Chromosome ◽  
Unexpected Event ◽  
Meiotic Sex Chromosome Inactivation ◽  
Ratio Distortion ◽  
High Fraction ◽  
Malaria Mosquitoes ◽  
Population Suppression

AbstractSynthetic sex-ratio distorters based on X-chromosome shredding are predicted to be more efficient than sterile males for population suppression of malaria mosquitoes using genetic control. X-chromosome shredding operates through the targeted elimination of X-chromosome-bearing gametes during male spermatogenesis, resulting in males that have a high fraction of male offspring. Strains harboring autosomal constructs containing a modified endonuclease I-PpoI have now been developed in the malaria mosquito Anopheles gambiae, resulting in strong sex-ratio distortion towards males. Data are being gathered for these strains for submission of regulatory dossiers for contained use and subsequent field release in West Africa. Since autosomal X-shredders are transmitted in a Mendelian fashion and can be selected against their frequency in the population is expected to decline once releases are halted. However, any unintended transfer of the X-shredder to the Y-chromosome could theoretically change these dynamics: This could lead to 100% transmission of the newly Y-linked X-shredder to the predominant male-biased offspring and its insulation from negative selection in females, resulting in its potential spread in the population and ultimately to suppression. Here, we analyze plausible mechanisms whereby an autosomal X-shredder could become linked to the Y-chromosome after release and provide data regarding its potential for activity should it become linked to the Y-chromosome. Our results strongly suggest that Y-chromosome linkage through remobilization of the transposon used for the initial genetic transformation is unlikely, and that, in the unexpected event that the X-shredder becomes linked to the Y-chromosome, expression and activity of the X-shredder would likely be inhibited by meiotic sex chromosome inactivation. We conclude that a functioning X-shredding-based Y-drive resulting from a naturally induced transposition or translocation of the transgene onto the Y-chromosome is unlikely.

scholarly journals Modifier Genes of the Sex Ratio Trait in Drosophila pseudoobscura

Genetics ◽  
1987 ◽  
Vol 116 (2) ◽  
pp. 275-283
Author(s):  
Gary Cobbs
Keyword(s):  
Sex Ratio ◽  
Y Chromosome ◽  
X Chromosome ◽  
High Frequency ◽  
Sex Chromosome ◽  
Drosophila Pseudoobscura ◽  
Sterile Male ◽  
Very High Frequency ◽  
Very High ◽  
Chromosome Nondisjunction

ABSTRACT The msr trait of Drosophila pseudoobscura occurs when "sex-ratio" males produce a very high frequency of null-X sperm which give rise to sterile male (X/O) progeny. The trait involves dramatically lowered fecundity due to spermiogenic failure. The msr trait is multigenic and the genes are located on autosomes II, III and IV of the L116 laboratory stock. This stock also carries genes on the Y chromosome that lower the level of msr. When the genes on the L116 autosomes are present together or with those on the Y chromosome of other stocks, they interact cooperatively to produce very high levels of msr. The msr genes require the presence of a sex-ratio X chromosome to have any effect and thus may be regarded as modifiers of the "sex-ratio" phenotype. Crosses show that the genes causing msr are primarily recessive but have some expression when heterozygous. Sex chromosome nondisjunction is proposed as the mechanism underlying the msr trait.

scholarly journals De novo assembly of a young Drosophila Y chromosome using Single-Molecule sequencing and Chromatin Conformation capture

2018 ◽  
Author(s):  
Shivani Mahajan ◽  
Kevin Wei ◽  
Matthew Nalley ◽  
Lauren Giblisco ◽  
Doris Bachtrog
Keyword(s):  
Y Chromosome ◽  
Single Molecule ◽  
Sex Chromosome ◽  
De Novo ◽  
Repetitive Sequences ◽  
Chromatin Interaction ◽  
Bac Clone ◽  
Long Reads ◽  
Y Chromosome Evolution ◽  
Genome Assemblies

While short-read sequencing technology has resulted in a sharp increase in the number of species with genome assemblies, these assemblies are typically highly fragmented. Repeats pose the largest challenge for reference genome assembly, and pericentromeric regions and the repeat-rich Y chromosome are typically ignored from sequencing projects. Here, we assemble the genome of Drosophila miranda using long reads for contig formation, chromatin interaction maps for scaffolding and short reads, optical mapping and BAC clone sequencing for consensus validation. Our assembly recovers entire chromosomes and contains large fractions of repetitive DNA, including ~41.5 Mb of pericentromeric and telomeric regions, and >100Mb of the recently formed highly repetitive neo-Y chromosome. While Y chromosome evolution is typically characterized by global sequence loss and shrinkage, the neo-Y increased in size by almost 3-fold, due to the accumulation of repetitive sequences. Our high-quality assembly allows us to reconstruct the chromosomal events that have led to the unusual sex chromosome karyotype in D. miranda, including the independent de novo formation of a pair of sex chromosomes at two distinct time points, or the reversion of a former Y chromosome to an autosome.

scholarly journals 344ICSI-MEDIATED GENE TRANSFER SKEWS SEX RATIO AGAINST FEMALE BIRTHS IN MICE

2004 ◽  
Vol 16 (2) ◽  
pp. 292
Author(s):  
P.N. Moreira ◽  
B. Pintado ◽  
L. Montoliu ◽  
A. Gutiérrez-Adán
Keyword(s):  
Gene Transfer ◽  
Sex Ratio ◽  
X Chromosome ◽  
Sex Chromosome ◽  
Single Gene ◽  
Transgenic Animals ◽  
Sperm Nucleus ◽  
Dna Molecules ◽  
Female Embryo ◽  
Foreign Dna

ICSI-mediated gene transfer has been used as an alternative method to pronuclear microinjection for the genomic modification of many species. With this method, transgenic embryos are produced by the microinjection of metaphase II oocytes with spermatozoa previously incubated with foreign DNA. Recently, it was shown in mice that the low percentage of transgenic animals produced from injected oocytes, results from the fact that the expression of foreign DNA is associated with paternal chromosome degradation (Szczygiel M.A. et al., 2003 Biol. Reprod. 68, 1903–1910). It is also known that sex chromosomes localize preferentially, at least in humans, on the periphery of the sperm nucleus on sub-acrosomal regions (Sbracia M. et al., 2002 Hum. Reprod. 17, 320–324), suggesting a high level of interaction with foreign DNA molecules with possible impact on the sex ratio of the offspring. In order to test this hypothesis we have compared ICSI (no DNA), and with ICSI-mediated EGFP (5Kb plasmid DNA from Clonetech, Spain) transfer, with ICSI-mediated YRT3 (a mouse tyrosinase gene derivative YAC-DNA with 100Kb; Montoliu L. et al., 1996 EMBO) transfer. Gametes were from 6–8 weeks old CD1 mice. ICSI-mediated gene transfer with post-thawed immotile spermatozoa, extended in M2 medium in the absence of ion chelators (EDTA and EGTA), was done as previously described (Szczygiel M.A. et al., 2003 Biol. Reprod. 68, 1903–1910). Table 1 below summarizes the data collected. Relative to our control, sex ratio deviation was a consequence of the coinjection of DNA. Forty-three percent of males were obtained with regular ICSI, whereas 64% and 65% were the respective percentages when EGFP or YRT3 DNA was coinjected with spermatozoa. This statistically significant (P<0.05, z-test, Sigma Stat, Jandel Scientific, USA) sex ratio deviation, favoring male ICSI offspring when foreign DNA is coinjected, may result from a higher female embryo susceptibility to parental sex chromosome fragmentation induced by the interaction with foreign DNA molecules. Possible impairment of X chromosome inactivation and dosage compensation resulting from the fragmentation of the sex chromosome on X-carrying spermatozoa could explain this female embryo degeneration. Supporting this view, it was recently shown in mice that sex ratio can be skewed against female births by a mutation in a single gene of the X chromosome (Tsix) involved in such mechanisms (Lee J.T., 2002 Nat. Genet.). In conclusion, mouse ICSI-mediated gene transfer induces sex ratio deviation favoring male offspring. Table 1 Sex ratio of the offspring obtained with ICSI, ICSI-mediated EGFP transfer, and ICSI-mediated YRT3 transfer

scholarly journals Bisection of the X chromosome disrupts the initiation of chromosome silencing during meiosis in Caenorhabditis elegans

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yisrael Rappaport ◽  
Hanna Achache ◽  
Roni Falk ◽  
Omer Murik ◽  
Oren Ram ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Rna Polymerase Ii ◽  
X Chromosome ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Transcription Analysis ◽  
X Chromosomes ◽  
Unique Character ◽  
Active Transcription ◽  
Heterogametic Sex

AbstractDuring meiosis, gene expression is silenced in aberrantly unsynapsed chromatin and in heterogametic sex chromosomes. Initiation of sex chromosome silencing is disrupted in meiocytes with sex chromosome-autosome translocations. To determine whether this is due to aberrant synapsis or loss of continuity of sex chromosomes, we engineered Caenorhabditis elegans nematodes with non-translocated, bisected X chromosomes. In early meiocytes of mutant males and hermaphrodites, X segments are enriched with euchromatin assembly markers and active RNA polymerase II staining, indicating active transcription. Analysis of RNA-seq data showed that genes from the X chromosome are upregulated in gonads of mutant worms. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, our data indicate that unsynapsed X segments are transcribed. Therefore, our results suggest that sex chromosome chromatin has a unique character that facilitates its meiotic expression when its continuity is lost, regardless of whether or not it is synapsed.

scholarly journals On the virulence of the entomopathogenic fungi, Beauveria bassiana and Metarhizium anisopliae (Ascomycota: Hypocreales), against the diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae)

2021 ◽  
Vol 31 (1) ◽  
Author(s):  
Muhammad Shehzad ◽  
Muhammad Tariq ◽  
Tariq Mukhtar ◽  
Asim Gulzar
Keyword(s):  
Sex Ratio ◽  
Beauveria Bassiana ◽  
Entomopathogenic Fungi ◽  
Plutella Xylostella ◽  
Metarhizium Anisopliae ◽  
Insect Pest ◽  
Diamondback Moth ◽  
Economic Damage ◽  
Offspring Sex Ratio ◽  
Development Of Resistance

Abstract Background The diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae), is a noxious pest of cruciferous crops all over the world causing serious economic damage. Management of insect pest generally depends on chemical control; however, due to development of resistance against all types of insecticides, alternative approaches especially utilization of a microbial agent is inevitable. Results Potential of 2 entomopathogenic fungi (EPF), viz., Beauveria bassiana and Metarhizium anisopliae, was evaluated against 2nd and 3rd larval instars of P. xylostella by adopting leaf dip and direct spraying methods under laboratory conditions. Significant mortality rate was achieved by each fungus under adopted methodologies. However, B. bassiana was found to be more effective in both conditions than M. anisopliae. Highest mean corrected mortality (77.80%) was recorded, when spores of B. bassiana were sprayed on the 2nd instar larvae (LC50=1.78×104/ml) after the 6th day of treatment. Similarly, incase of M. anisopliae LC50 for the 2nd instar at the same methodology was 2.78×104/ml with a mortality percentage of 70.0%. Offspring sex ratio was non-significantly related to treatment concentration and methodology, except for the control. Conclusion Beauveria bassiana and M. anisopliae had potential to suppress P. xylostella infestations when applied appropriately. Present findings suggested that B. bassiana and M. anisopliae when sprayed on immatures of host insect had more effect as compared to leaf dip procedure. Furthermore, no significant effect of concentrations was observed on sex ratio.

scholarly journals Deficit of Mitonuclear Genes on the Human X Chromosome Predates Sex Chromosome Formation

2015 ◽  
Vol 7 (2) ◽  
pp. 636-641 ◽  
Author(s):  
Rebecca Dean ◽  
Fabian Zimmer ◽  
Judith E. Mank
Keyword(s):  
X Chromosome ◽  
Sex Chromosome ◽  
Chromosome Formation

scholarly journals Absence of X-chromosome dosage compensation in the primordial germ cells of Drosophila embryos

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ryoma Ota ◽  
Makoto Hayashi ◽  
Shumpei Morita ◽  
Hiroki Miura ◽  
Satoru Kobayashi
Keyword(s):  
X Chromosome ◽  
Germ Cells ◽  
Dosage Compensation ◽  
Sex Chromosome ◽  
Primordial Germ Cells ◽  
Histone H4 ◽  
X Chromosomes ◽  
Essential Components ◽  
Msl Complex ◽  
Male Specific

AbstractDosage compensation is a mechanism that equalizes sex chromosome gene expression between the sexes. In Drosophila, individuals with two X chromosomes (XX) become female, whereas males have one X chromosome (XY). In males, dosage compensation of the X chromosome in the soma is achieved by five proteins and two non-coding RNAs, which assemble into the male-specific lethal (MSL) complex to upregulate X-linked genes twofold. By contrast, it remains unclear whether dosage compensation occurs in the germline. To address this issue, we performed transcriptome analysis of male and female primordial germ cells (PGCs). We found that the expression levels of X-linked genes were approximately twofold higher in female PGCs than in male PGCs. Acetylation of lysine residue 16 on histone H4 (H4K16ac), which is catalyzed by the MSL complex, was undetectable in these cells. In male PGCs, hyperactivation of X-linked genes and H4K16ac were induced by overexpression of the essential components of the MSL complex, which were expressed at very low levels in PGCs. Together, these findings indicate that failure of MSL complex formation results in the absence of X-chromosome dosage compensation in male PGCs.

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